/** This test requires manual intervention to provide an appropriate file to read and write. */
void test_stream()
{
FILE* fp = fopen("/tmp/opsec.p12", "r");
FILE* fpo;
zstr z1 = z_slurp_stream(fp);
zstr z2;
fpo = fopen("/tmp/opsec.p12.out", "w");
cz_to_stream(cz(z1), fpo);
fflush(fpo);
fclose(fpo);
z2 = z_slurp_stream(fopen("/tmp/opsec.p12.out", "r"));
assert (zeq(cz(z1), cz(z2)));
}
void Foam::linearValveLayersFvMesh::addZonesAndModifiers()
{
// Add zones and modifiers for motion action
if
(
pointZones().size() > 0
|| faceZones().size() > 0
|| cellZones().size() > 0
)
{
Info<< "void linearValveLayersFvMesh::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
if (topoChanger_.size() == 0)
{
FatalErrorIn
(
"void linearValveLayersFvMesh::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
return;
}
Info<< "Time = " << time().timeName() << endl
<< "Adding zones and modifiers to the mesh" << endl;
// Add zones
List<pointZone*> pz(1);
List<faceZone*> fz(4);
List<cellZone*> cz(0);
// Add an empty zone for cut points
pz[0] = new pointZone
(
"cutPointZone",
labelList(0),
0,
pointZones()
);
// Do face zones for slider
// Inner slider
const word innerSliderName(motionDict_.subDict("slider").lookup("inside"));
const polyPatch& innerSlider =
boundaryMesh()[boundaryMesh().findPatchID(innerSliderName)];
labelList isf(innerSlider.size());
forAll (isf, i)
{
isf[i] = innerSlider.start() + i;
}
void Foam::mixerGgiFvMesh::addZonesAndModifiers()
{
// Add zones and modifiers for motion action
if (cellZones().size() > 0)
{
Info<< "void mixerGgiFvMesh::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
return;
}
Info<< "Time = " << time().timeName() << endl
<< "Adding zones and modifiers to the mesh" << endl;
// Add zones
List<pointZone*> pz(0);
List<faceZone*> fz(0);
List<cellZone*> cz(1);
// Copy the face zones associated with the GGI interfaces
if (faceZones().size() > 0)
{
// Copy face zones
Info << "Copying existing face zones" << endl;
fz.setSize(faceZones().size());
forAll (faceZones(), i)
{
fz[i] = faceZones()[i].clone(faceZones()).ptr();
}
//-----------------------------------------------------------------------------
int sample_d(mglGraph *gr)
{
mglData a(50,50),b(50,50);
mglData cx(50,50,50),cy(50,50,50),cz(50,50,50);
a.Modify("0.6*sin(2*pi*x)*sin(3*pi*y) + 0.4*cos(3*pi*(x*y))");
b.Modify("0.6*cos(2*pi*x)*cos(3*pi*y) + 0.4*cos(3*pi*(x*y))");
cx.Modify("0.01*(x-0.3)/pow((x-0.3)^2+(y-0.5)^2+(z-0.5)^2,1.5) - 0.01*(x-0.7)/pow((x-0.7)^2+(y-0.5)^2+(z-0.5)^2,1.5)");
cy.Modify("0.01*(y-0.5)/pow((x-0.3)^2+(y-0.5)^2+(z-0.5)^2,1.5) - 0.01*(y-0.5)/pow((x-0.7)^2+(y-0.5)^2+(z-0.5)^2,1.5)");
cz.Modify("0.01*(z-0.5)/pow((x-0.3)^2+(y-0.5)^2+(z-0.5)^2,1.5) - 0.01*(z-0.5)/pow((x-0.7)^2+(y-0.5)^2+(z-0.5)^2,1.5)");
gr->NewFrame();
gr->Box(); gr->Axis("xy");
gr->Puts(mglPoint(0,1.2,1),"Vector field (color ~ \\sqrt{a^2})","rC",8);
gr->Vect(a,b,"","value 50");
gr->EndFrame();
gr->NewFrame();
gr->Box(); gr->Axis("xy");
gr->Puts(mglPoint(0,1.2,1),"Vector field (length ~ \\sqrt{a^2})","rC",8);
gr->Vect(a,b);
gr->EndFrame();
gr->NewFrame();
gr->Box(); gr->Axis("xy");
gr->Puts(mglPoint(0,1.2,1),"Flow chart (blue - source)","rC",8);
gr->Flow(a,b);
gr->EndFrame();
return gr->GetNumFrame();
}
void
post_compl(Home home, SetView x, SetOpType op, SetView y, ConstSetView z) {
GlbRanges<ConstSetView> zr(z);
RangesCompl<GlbRanges<ConstSetView> > zrc(zr);
IntSet zc(zrc);
ConstSetView cz(home, zc);
rel_eq<SetView,SetView,ConstSetView>(home, x, op, y, cz);
}
int test_repr()
{
zstr z2;
czstr z = cs_as_cz("k");
zstr rz = repr(z);
#ifndef NDEBUG
const czstr a = cs_as_cz("\\\\k");
#endif
assert (!strcmp((const char*)rz.buf, "k"));
z = cs_as_cz("\\k");
assert (z.len == 2);
free_z(rz);
rz = repr(z);
assert (rz.len == 3);
assert (a.len == 3);
assert (!strcmp((const char*)rz.buf, "\\\\k"));
assert (zeq(cz(rz), a));
z2 = new_z(4);
z2.buf[0] = 1;
z2.buf[1] = 10;
z2.buf[2] = 100;
z2.buf[3] = 252;
free_z(rz);
rz = repr(cz(z2));
assert (!strcmp((const char*)rz.buf, "\\x01\\x0ad\\xfc"));
free_z(z2);
z2 = new_z(1);
z2.buf[0] = '\0';
free_z(rz);
rz = repr(cz(z2));
assert (!strcmp((const char*)rz.buf, "\\x00"));
free_z(z2);
free_z(rz);
return 0;
}
int test_czstr()
{
zstr a = cs_as_z("abcdefgh");
czstr b = cz(a);
printf("%d:%s\n", b.len, b.buf);
/*b.len = 5;*/ /* should be a compile error since b is const. */
/*b.buf = NULL;*/ /* should be a compile error since b is const. */
/*b.buf[0] = '\0';*/ /* should be a compile error since b is a czstr. */
return 0;
}
double CZ(short state, double zmeas, double z0, double d0, double L, double (*Psi)(double z)){
double c;
FILE *f;
if(state==1){ //both instability and stability considered
c=cz(zmeas,z0,d0,L,(Psi),(*PsiStab));
}else if(state==2){ //instability considered & stability not considered
c=cz(zmeas,z0,d0,L,(Psi),(*Zero));
}else if(state==3){ //instability not considered & stability considered
c=cz(zmeas,z0,d0,L,(*Zero),(*PsiStab));
}else if(state==4){ //both instability and stability not considered
c=cz(zmeas,z0,d0,L,(*Zero),(*Zero));
}else{
f = fopen(FailedRunFile, "w");
fprintf(f,"Error:: Value of state turbulence not admitted\n");
fclose(f);
t_error("Fatal Error! Geotop is closed. See failing report.");
c = 0.0;
}
return(c);
}
int main(){
char** word=cz(MAX);
count* ct=sz(MAX);
int i=0;
for (i=0;i<MAX;++i){
word[i]=NULL;
ct[i].pv=0;
}
create(word,ct);
deal(word,ct);
HeapSort(ct,MAX);
sortput(word,ct);
return 0;
}
std::vector<ChebSegment> CFunctionToBspline::CFunctionToBsplineImpl::approxSegment(double umin, double umax, int depth)
{
// to estimate the error, we do a chebycheff approximation at higher
// degree and evaluate the coefficients
int K = _degree + 4;
double alpha = 0.5;
math_Vector cx = cheb_approx(_xfunc, K+1, umin, umax);
math_Vector cy = cheb_approx(_yfunc, K+1, umin, umax);
math_Vector cz = cheb_approx(_zfunc, K+1, umin, umax);
// estimate error
double errx=0., erry = 0., errz = 0.;
for (int i = _degree+1; i < K+1; ++i) {
errx += fabs(cx(i));
erry += fabs(cy(i));
errz += fabs(cz(i));
}
double error = sqrt(errx*errx + erry*erry + errz*errz);
if (error < _tol || depth >= _maxDepth) {
// we can use this approximation, store to structure
ChebSegment seg(_degree);
seg.cx = subVec(cx, 0, _degree);
seg.cy = subVec(cy, 0, _degree);
seg.cz = subVec(cz, 0, _degree);
seg.error = error;
seg.umin = umin;
seg.umax = umax;
std::vector<ChebSegment> list;
list.push_back(seg);
return list;
}
else {
// we have to split the range in two parts and do the approximation for each of them
std::vector<ChebSegment> list1 = approxSegment(umin, umin + (umax-umin)*alpha, depth + 1);
std::vector<ChebSegment> list2 = approxSegment(umin + (umax-umin)*alpha, umax, depth + 1);
// combine lists
list1.insert(list1.end(), list2.begin(), list2.end());
return list1;
}
}
void Foam::multiMixerFvMesh::addZonesAndModifiers()
{
// Add zones and modifiers for motion action
if
(
pointZones().size() > 0
|| faceZones().size() > 0
|| cellZones().size() > 0
)
{
Info<< "void multiMixerFvMesh::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
if (topoChanger_.size() == 0 && useTopoSliding())
{
FatalErrorIn
(
"void multiMixerFvMesh::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
return;
}
Info<< "Time = " << time().timeName() << endl
<< "Adding zones and modifiers to the mesh. " << rotors_.size()
<< " sliders found" << endl;
DynamicList<pointZone*> pz(rotors_.size());
DynamicList<faceZone*> fz(3*rotors_.size());
DynamicList<cellZone*> cz(rotors_.size());
// Create region split: mark every cell with its topological region
regionSplit rs(*this);
Info << "Adding point, face and cell zones" << endl;
forAll (rotors_, rotorI)
{
rotors_[rotorI].addZones(pz, fz, cz, rs);
}
void
MainWindow::newPoints(int n)
{
scene.periodic_triangulation.clear();
scene.points.clear();
CGAL::Random rnd(std::time(NULL));
CGAL::Random_points_in_cube_3<Point_3, Creator> in_cube(1,rnd);
for (int i=0 ; i<n ; i++)
if (scene.two_dimensional) {
Point_3 rdpt = *in_cube++;
scene.points.push_back(Point_3(rdpt.x(),rdpt.y(),0.));
} else
scene.points.push_back(*in_cube++);
Iso_cuboid_3 dom(-1,-1,-1,1,1,1);
scene.periodic_triangulation.set_domain(dom);
scene.periodic_triangulation.insert(scene.points.begin(), scene.points.end());
FT cx(0),cy(0),cz(0);
for (int i=0 ; i<8 ; i++) {
cx += dom[i].x();
cy += dom[i].y();
cy += dom[i].y();
}
qglviewer::Vec center(cx/8.,cy/8.,cz/8.);
viewer->setSceneCenter(center);
viewer->setSceneRadius(std::sqrt(
((dom.xmax()-dom.xmin())*(dom.xmax()-dom.xmin()))
+ ((dom.xmax()-dom.xmin())*(dom.xmax()-dom.xmin()))
+ ((dom.xmax()-dom.xmin())*(dom.xmax()-dom.xmin()))));
speedSlider->setRange(0,100);
speedSlider->setSliderPosition(100);
emit (sceneChanged());
}
void
MainWindow::loadPoints()
{
QString fileName = QFileDialog
::getOpenFileName(this, tr("Open point set"),
".", tr("All files (*)"));
if(fileName.isEmpty()) return;
std::ifstream ifs(fileName.toLatin1().data() );
scene.points.clear();
Iso_cuboid_3 dom;
ifs >> dom;
std::copy(std::istream_iterator<Point_3>(ifs),
std::istream_iterator<Point_3>(),
std::back_inserter(scene.points));
scene.periodic_triangulation.set_domain(dom);
scene.periodic_triangulation.insert(scene.points.begin(), scene.points.end());
FT cx(0),cy(0),cz(0);
for (int i=0 ; i<8 ; i++) {
cx += dom[i].x();
cy += dom[i].y();
cy += dom[i].y();
}
qglviewer::Vec center(cx/8.,cy/8.,cz/8.);
viewer->setSceneCenter(center);
viewer->setSceneRadius(std::sqrt(
((dom.xmax()-dom.xmin())*(dom.xmax()-dom.xmin()))
+ ((dom.xmax()-dom.xmin())*(dom.xmax()-dom.xmin()))
+ ((dom.xmax()-dom.xmin())*(dom.xmax()-dom.xmin()))));
speedSlider->setRange(0,100);
speedSlider->setSliderPosition(100);
emit (sceneChanged());
}
void
post_compl(Home home, SetView x, SetOpType op, SetView y, SetView z) {
ComplementView<SetView> cz(z);
rel_eq<SetView,SetView,ComplementView<SetView> >(home, x, op, y, cz);
}
void Foam::sixDofTopoMotion::addZonesAndModifiers()
{
// Add zones and modifiers for motion action
if (useTopoSliding_)
{
if
(
pointZones().size() > 0
|| faceZones().size() > 0
|| cellZones().size() > 0
)
{
Info<< "void sixDofTopoMotion::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
if (topoChanger_.size() == 0)
{
FatalErrorIn
(
"void sixDofTopoMotion::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
return;
}
Info<< "Time = " << time().timeName() << endl
<< "Adding zones and modifiers to the mesh" << endl;
// Add zones
List<pointZone*> pz(3*bodies_.size());
List<faceZone*> fz(3*bodies_.size());
List<cellZone*> cz(0);
label npz = 0;
label nfz = 0;
label nSliders = 0;
forAll (bodies_, bodyI)
{
const floatingBody& curBody = bodies_[bodyI];
if
(
curBody.hullSlider().active()
&& curBody.fixedSlider().active()
)
{
nSliders++;
// Add an empty zone for cut points
pz[npz] = new pointZone
(
curBody.name() + "CutPointZone",
labelList(0),
npz,
pointZones()
);
npz++;
// Do face zones for slider
// Inner slider
const polyPatch& innerSlider =
boundaryMesh()[curBody.hullSlider().index()];
labelList isf(innerSlider.size());
forAll (isf, i)
{
isf[i] = innerSlider.start() + i;
}
fz[nfz] = new faceZone
(
curBody.name() + "InsideSliderZone",
isf,
boolList(innerSlider.size(), false),
nfz,
faceZones()
);
nfz++;
// Outer slider
const polyPatch& outerSlider =
boundaryMesh()[curBody.fixedSlider().index()];
labelList osf(outerSlider.size());
forAll (osf, i)
{
osf[i] = outerSlider.start() + i;
}
fz[nfz] = new faceZone
(
curBody.name() + "OutsideSliderZone",
osf,
boolList(outerSlider.size(), false),
nfz,
faceZones()
);
nfz++;
// Add empty zone for cut faces
fz[nfz] = new faceZone
(
curBody.name() + "CutFaceZone",
labelList(0),
boolList(0, false),
nfz,
faceZones()
);
nfz++;
}
void Foam::simpleTwoStroke::addZonesAndModifiers()
{
// Add the zones and mesh modifiers to operate piston motion
if
(
pointZones().size() > 0
|| faceZones().size() > 0
|| cellZones().size() > 0
)
{
Info<< "Time = " << engTime().theta() << endl;
Info<< "void simpleTwoStroke::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
if (topoChanger_.size() == 0)
{
FatalErrorIn
(
"void simpleTwoStroke::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
setVirtualPistonPosition();
checkAndCalculate();
return;
}
Info << "checkAndCalculate()" << endl;
checkAndCalculate();
Info<< "Time = " << engTime().theta() << endl
<< "Adding zones to the engine mesh" << endl;
//fz = 4: virtual piston, outSidePort, insidePort, cutFaceZone
//pz = 2: piston points, cutPointZone
//cz = 1: moving mask
List<pointZone*> pz(3);
List<faceZone*> fz(4);
List<cellZone*> cz(1);
label nPointZones = 0;
label nFaceZones = 0;
label nCellZones = 0;
// Add the piston zone
if (piston().patchID().active())
{
// Piston position
Info << "Adding face zone for piston layer addition/removal" << endl;
label pistonPatchID = piston().patchID().index();
scalar zPist =
max(boundary()[pistonPatchID].patch().localPoints()).z();
scalar zPistV = zPist + offSet();
labelList zone1(faceCentres().size());
boolList flipZone1(faceCentres().size(), false);
label nZoneFaces1 = 0;
bool foundAtLeastOne = false;
scalar zHigher = GREAT;
scalar dh = GREAT;
scalar dl = GREAT;
forAll (faceCentres(), faceI)
{
// The points have to be in the cylinder and not in the ports....
scalar zc = faceCentres()[faceI].z();
scalar xc = faceCentres()[faceI].x();
scalar yc = faceCentres()[faceI].y();
vector n = faceAreas()[faceI]/mag(faceAreas()[faceI]);
scalar dd = n & vector(0,0,1);
if(sqrt(sqr(xc)+sqr(yc)) < 0.5 * engTime().bore().value())
{
if (dd > 0.1)
{
if (zPistV - zc > 0 && zPistV - zc < dl)
{
dl = zPistV - zc;
}
if (zc - zPistV > 0 && zc - zPistV < dh)
{
zHigher = zc;
dh = zc - zHigher;
}
if
(
zc > zPistV - delta()
&& zc < zPistV + delta()
)
{
foundAtLeastOne = true;
if ((faceAreas()[faceI] & vector(0,0,1)) < 0)
{
flipZone1[nZoneFaces1] = true;
}
zone1[nZoneFaces1] = faceI;
nZoneFaces1++;
}
}
}
}
void Foam::linearValveLayersFvMesh::addZonesAndModifiers()
{
// Inner slider
const word innerSliderName(motionDict_.subDict("slider").lookup("inside"));
// Outer slider
const word outerSliderName
(
motionDict_.subDict("slider").lookup("outside")
);
bool initialised = false;
// Check if zones and modifiers for motion action are present
label insideZoneID = faceZones().findZoneID(innerSliderName + "Zone");
label outsideZoneID = faceZones().findZoneID(outerSliderName + "Zone");
if
(
insideZoneID > -1
|| outsideZoneID > -1
)
{
// Zones found. Check topo changer
if (topoChanger_.empty())
{
FatalErrorIn
(
"void linearValveLayersFvMesh::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
initialised = true;
}
// Check if slider has been initialised on any of the processors
reduce(initialised, orOp<bool>());
if (initialised)
{
InfoIn("void linearValveLayersFvMesh::addZonesAndModifiers()")
<< "Zones and modifiers already present. Skipping."
<< endl;
return;
}
// Add zones and modifiers for motion action
Info<< "Time = " << time().timeName() << endl
<< "Adding zones and modifiers to the mesh" << endl;
// Add zones
label nPz = 0;
label nFz = 0;
label nCz = 0;
List<pointZone*> pz(pointZones().size() + 1);
List<faceZone*> fz(faceZones().size() + 4);
List<cellZone*> cz(cellZones().size());
// Add a topology modifier
topoChanger_.setSize(2);
label nTc = 0;
// Copy existing point zones
forAll (pointZones(), zoneI)
{
pz[nPz] = pointZones()[zoneI].clone(pointZones()).ptr();
nPz++;
}
void Foam::layerAR::addZonesAndModifiers()
{
// Add the zones and mesh modifiers to operate piston motion
if
(
pointZones().size() > 0
|| faceZones().size() > 0
|| cellZones().size() > 0
)
{
Info<< "void layerAR::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
if (topoChanger_.size() == 0)
{
FatalErrorIn
(
"void layerAR::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
setVirtualPistonPosition();
checkAndCalculate();
return;
}
checkAndCalculate();
Info<< "Time = " << engTime().theta() << endl
<< "Adding zones to the engine mesh" << endl;
//fz = 1: faces where layer are added/removed
//pz = 2: points below the virtual piston faces and head points
List<pointZone*> pz(2);
List<faceZone*> fz(1);
List<cellZone*> cz(0);
label nPointZones = 0;
label nFaceZones = 0;
// Add the piston zone
if (piston().patchID().active() && offSet() > SMALL)
{
// Piston position
label pistonPatchID = piston().patchID().index();
scalar zPist = max(boundary()[pistonPatchID].patch().localPoints()).z();
scalar zPistV = zPist + offSet();
labelList zone1(faceCentres().size());
boolList flipZone1(faceCentres().size(), false);
label nZoneFaces1 = 0;
bool foundAtLeastOne = false;
scalar zHigher = GREAT;
scalar dh = GREAT;
scalar dl = GREAT;
forAll (faceCentres(), faceI)
{
scalar zc = faceCentres()[faceI].z();
vector n = faceAreas()[faceI]/mag(faceAreas()[faceI]);
scalar dd = n & vector(0,0,1);
if (dd > 0.1)
{
if (zPistV - zc > 0 && zPistV - zc < dl)
{
dl = zPistV - zc;
}
if (zc - zPistV > 0 && zc - zPistV < dh)
{
zHigher = zc;
dh = zc - zHigher;
}
if
(
zc > zPistV - delta()
&& zc < zPistV + delta()
)
{
foundAtLeastOne = true;
if ((faceAreas()[faceI] & vector(0,0,1)) < 0)
{
flipZone1[nZoneFaces1] = true;
}
zone1[nZoneFaces1] = faceI;
nZoneFaces1++;
}
}
}
int main(){
std::vector <int> mat(0);
std::vector <int> cat(0);
std::vector <double> cx(0);
std::vector <double> cy(0);
std::vector <double> cz(0);
std::vector <std::string> type(0);
std::vector <std::string> filenames(0);
// open coordinate file
std::ifstream coord_file;
coord_file.open("atoms-coords.cfg");
// read in file header
std::string dummy;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
// get number of atoms
unsigned int n_atoms;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+17);
n_atoms=atoi(dummy.c_str());
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
// get number of subsidiary files
unsigned int n_files;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+22);
n_files=atoi(dummy.c_str());
for(int file=0; file<n_files; file++){
getline(coord_file,dummy);
filenames.push_back(dummy);
//std::cout << filenames[file] << std::endl;
}
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
unsigned int n_local_atoms;
getline(coord_file,dummy);
//std::cout << dummy << std::endl;
n_local_atoms=atoi(dummy.c_str());
// resize arrays
mat.resize(n_atoms);
cat.resize(n_atoms);
cx.resize(n_atoms);
cy.resize(n_atoms);
cz.resize(n_atoms);
type.resize(n_atoms);
unsigned int counter=0;
// finish reading master file coordinates
for(int i=0;i<n_local_atoms;i++){
coord_file >> mat[counter] >> cat[counter] >> cx[counter] >> cy[counter] >> cz[counter] >> type[counter];
counter++;
}
// close master file
coord_file.close();
// now read subsidiary files
for(int file=0; file<n_files; file++){
std::ifstream infile;
infile.open(filenames[file].c_str());
// read number of atoms in this file
getline(infile,dummy);
n_local_atoms=atoi(dummy.c_str());
for(int i=0;i<n_local_atoms;i++){
infile >> mat[counter] >> cat[counter] >> cx[counter] >> cy[counter] >> cz[counter] >> type[counter];
counter++;
}
// close subsidiary file
infile.close();
}
// check for correct read in of coordinates
if(counter!=n_atoms) std::cerr << "Error in reading in coordinates" << std::endl;
// Loop over all possible spin config files
int ios = 0;
int spinfile_counter=0;
while(ios==0){
std::stringstream file_sstr;
file_sstr << "atoms-";
file_sstr << std::setfill('0') << std::setw(8) << spinfile_counter;
file_sstr << ".cfg";
std::string cfg_file = file_sstr.str();
//const char* cfg_filec = cfg_file.c_str();
std::ifstream spinfile;
spinfile.open(cfg_file.c_str());
if(spinfile.is_open()){
std::cout << "Processing file: " << cfg_file << std::endl;
// Read in file header
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
// get number of atoms
unsigned int n_spins;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+17);
n_spins=atoi(dummy.c_str());
if(n_spins!=n_atoms) std::cerr << "Error! - mismatch between number of atoms in coordinate and spin files" << std::endl;
getline(spinfile,dummy); // sys dimensions
//std::cout << dummy << std::endl;
char const field_delim = '\t';
dummy.erase (dummy.begin(), dummy.begin()+18);
std::istringstream ss(dummy);
std::vector<double> val(0);
for (std::string num; getline(ss, num, field_delim); ) {
val.push_back(atof(num.c_str()));
//std::cout << num << "\t" << val << std::endl;
}
double dim[3] = {val[0],val[1],val[2]};
//std::cout << dim[0] << "\t" << dim[1] << "\t" << dim[2] << std::endl;
getline(spinfile,dummy); // coord file
getline(spinfile,dummy); // time
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+5);
double time = atof(dummy.c_str());
getline(spinfile,dummy); // field
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+6);
double field = atof(dummy.c_str());
getline(spinfile,dummy); // temp
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+12);
double temperature = atof(dummy.c_str());
// magnetisation
getline(spinfile,dummy);
dummy.erase (dummy.begin(), dummy.begin()+14);
std::istringstream ss2(dummy);
val.resize(0);
for (std::string num; getline(ss2, num, field_delim); ) {
val.push_back(atof(num.c_str()));
//std::cout << num << "\t" << val << std::endl;
}
double mx = val[0];
double my = val[1];
double mz = val[2];
// get number of materials
unsigned int n_mat;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+20);
n_mat=atoi(dummy.c_str());
std::vector <material_t> material(n_mat);
for(int imat=0;imat<n_mat;imat++){
getline(spinfile,dummy);
//dummy.erase (dummy.begin(), dummy.begin()+22);
std::istringstream ss(dummy);
std::vector<double> val(0);
for (std::string num; getline(ss, num, field_delim); ) {
val.push_back(atof(num.c_str()));
}
material[imat].mu_s = val[0];
material[imat].mx = val[1];
material[imat].my = val[2];
material[imat].mz = val[3];
material[imat].magm = val[4];
//std::cout << material[imat].mu_s << "\t" << material[imat].mx << "\t" << material[imat].my << "\t" << material[imat].mz << "\t" << material[imat].magm << std::endl;
}
// line
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
// get number of subsidiary files
unsigned int n_files;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
dummy.erase (dummy.begin(), dummy.begin()+22);
n_files=atoi(dummy.c_str());
filenames.resize(0);
for(int file=0; file<n_files; file++){
getline(spinfile,dummy);
filenames.push_back(dummy);
//std::cout << filenames[file] << std::endl;
}
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
unsigned int n_local_atoms;
getline(spinfile,dummy);
//std::cout << dummy << std::endl;
n_local_atoms=atoi(dummy.c_str());
// Open Povray Include File
std::stringstream incpov_file_sstr;
incpov_file_sstr << "atoms-";
incpov_file_sstr << std::setfill('0') << std::setw(8) << spinfile_counter;
incpov_file_sstr << ".inc";
std::string incpov_file = incpov_file_sstr.str();
// Open Povray Output file
std::stringstream pov_file_sstr;
pov_file_sstr << "atoms-";
pov_file_sstr << std::setfill('0') << std::setw(8) << spinfile_counter;
pov_file_sstr << ".pov";
std::string pov_file = pov_file_sstr.str();
std::ofstream pfile;
pfile.open(pov_file.c_str());
// Ouput povray file header
double size, mag_vec;
double vec[3];
size = sqrt(dim[0]*dim[0] + dim[1]*dim[1] + dim[2]*dim[2]);
vec[0] = (1.0/dim[0]);
vec[1] = (1.0/dim[1]);
vec[2] = (1.0/dim[2]);
mag_vec = sqrt(vec[0]*vec[0]+vec[1]*vec[1]+vec[2]*vec[2]);
vec[0]/=mag_vec;
vec[1]/=mag_vec;
vec[2]/=mag_vec;
pfile << "#include \"colors.inc\"" << std::endl;
pfile << "#include \"metals.inc\"" << std::endl;
pfile << "#include \"screen.inc\"" << std::endl;
pfile << "#declare LX=" << dim[0]*0.5 << ";" << std::endl;
pfile << "#declare LY=" << dim[1]*0.5 << ";" << std::endl;
pfile << "#declare LZ=" << dim[2]*0.5 << ";" << std::endl;
pfile << "#declare CX=" << size*vec[0]*6.0 << ";" << std::endl;
pfile << "#declare CY=" << size*vec[1]*6.0 << ";" << std::endl;
pfile << "#declare CZ=" << size*vec[2]*6.0 << ";" << std::endl;
pfile << "#declare ref=0.4;" << std::endl;
pfile << "global_settings { assumed_gamma 2.0 }" << std::endl;
pfile << "background { color Gray30 }" << std::endl;
pfile << "Set_Camera(<CX,CY,CZ>, <LX,LY,LZ>, 15)" << std::endl;
pfile << "Set_Camera_Aspect(4,3)" << std::endl;
pfile << "Set_Camera_Sky(<0,0,1>)" << std::endl;
pfile << "light_source { <2*CX, 2*CY, 2*CZ> color White}" << std::endl;
for(int imat=0;imat<n_mat;imat++){
pfile << "#declare sscale"<< imat << "=2.0;" << std::endl;
pfile << "#declare rscale"<< imat << "=1.2;" << std::endl;
pfile << "#declare cscale"<< imat << "=3.54;" << std::endl;
pfile << "#declare cones"<< imat << "=0;" << std::endl;
pfile << "#declare arrows"<< imat << "=1;" << std::endl;
pfile << "#declare spheres"<< imat << "=1;" << std::endl;
pfile << "#declare cubes" << imat << "=0;" << std::endl;
pfile << "#declare spincolors"<< imat << "=1;" << std::endl;
pfile << "#declare spincolor"<< imat << "=pigment {color rgb < 0.1 0.1 0.1 >};" << std::endl;
pfile << "#macro spinm"<< imat << "(cx,cy,cz,sx,sy,sz, cr,cg,cb)" << std::endl;
pfile << "union{" << std::endl;
pfile << "#if(spheres" << imat << ") sphere {<cx,cy,cz>,0.5*rscale"<< imat << "} #end" << std::endl;
pfile << "#if(cubes" << imat << ") box {<cx-cscale"<< imat << "*0.5,cy-cscale" << imat << "*0.5,cz-cscale"<< imat << "*0.5>,<cx+cscale"<< imat << "*0.5,cy+cscale" << imat << "*0.5,cz+cscale"<< imat << "*0.5>} #end" << std::endl;
pfile << "#if(cones"<< imat << ") cone {<cx+0.5*sx*sscale0,cy+0.5*sy*sscale"<< imat << ",cz+0.5*sz*sscale"<< imat << ">,0.0 <cx-0.5*sx*sscale"<< imat << ",cy-0.5*sy*sscale"<< imat << ",cz-0.5*sz*sscale"<< imat << ">,sscale0*0.5} #end" << std::endl;
pfile << "#if(arrows" << imat << ") cylinder {<cx+sx*0.5*sscale"<< imat <<",cy+sy*0.5*sscale"<< imat <<",cz+sz*0.5*sscale"<< imat <<
">,<cx-sx*0.5*sscale"<< imat <<",cy-sy*0.5*sscale"<< imat <<",cz-sz*0.5*sscale"<< imat <<">,sscale"<< imat <<"*0.12}";
pfile << "cone {<cx+sx*0.5*1.6*sscale"<< imat <<",cy+sy*0.5*1.6*sscale"<< imat <<",cz+sz*0.5*1.6*sscale"<< imat <<">,sscale"<< imat <<"*0.0 <cx+sx*0.5*sscale"<< imat <<
",cy+sy*0.5*sscale"<< imat <<",cz+sz*0.5*sscale"<< imat <<">,sscale"<< imat <<"*0.2} #end" << std::endl;
pfile << "#if(spincolors"<< imat << ") texture { pigment {color rgb <cr cg cb>}finish {reflection {ref} diffuse 1 ambient 0}}" << std::endl;
pfile << "#else texture { spincolor"<< imat << " finish {reflection {ref} diffuse 1 ambient 0}} #end" << std::endl;
pfile << "}" << std::endl;
pfile << "#end" << std::endl;
}
pfile << "#include \"" << incpov_file_sstr.str() << "\"" << std::endl;
pfile.close();
std::ofstream incpfile;
incpfile.open(incpov_file.c_str());
double sx,sy,sz,red,green,blue,ireal;
unsigned int si=0;
// Read in spin coordinates and output to povray file
for(int i=0; i<n_local_atoms;i++){
spinfile >> sx >> sy >> sz;
rgb(sz,red,green,blue);
incpfile << "spinm"<< mat[si] << "(" << cx[si] << "," << cy[si] << "," << cz[si] << ","
<< sx << "," << sy << "," << sz << "," << red << "," << green << "," << blue << ")" << std::endl;
si++;
}
// close master file
spinfile.close();
// now read subsidiary files
for(int file=0; file<n_files; file++){
std::ifstream infile;
infile.open(filenames[file].c_str());
// read number of atoms in this file
getline(infile,dummy);
n_local_atoms=atoi(dummy.c_str());
for(int i=0;i<n_local_atoms;i++){
infile >> sx >> sy >> sz;
rgb(sz,red,green,blue);
incpfile << "spinm"<< mat[si] << "(" << cx[si] << "," << cy[si] << "," << cz[si] << ","
<< sx << "," << sy << "," << sz << "," << red << "," << green << "," << blue << ")" << std::endl;
si++;
}
// close subsidiary file
infile.close();
}
// close povray inc file
incpfile.close();
spinfile_counter++;
}
else ios=1;
void Foam::simpleEngineTopoFvMesh::addZonesAndModifiers()
{
// Add the zones and mesh modifiers to operate piston and valve motion
if
(
pointZones().size() > 0
|| faceZones().size() > 0
|| cellZones().size() > 0
)
{
Info<< "void Foam::simpleEngineTopoFvMesh::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
if (topoChanger_.size() == 0)
{
FatalErrorIn
(
"void simpleEngineTopoFvMesh::addZonesAndModifiers()"
) << "Mesh modifiers not read properly"
<< abort(FatalError);
}
return;
}
Info<< "Time = " << engineTime_.theta() << endl
<< "Adding zones to the engine mesh" << endl;
List<pointZone*> pz(nValves());
List<faceZone*> fz(6*nValves() + 1);
List<cellZone*> cz(0);
label nPointZones = 0;
label nFaceZones = 0;
for (label valveI = 0; valveI < nValves(); valveI++)
{
// If both sides of the interface exist, add sliding interface
// for a valve
if
(
valves_[valveI].curtainInCylinderPatchID().active()
&& valves_[valveI].curtainInPortPatchID().active()
)
{
Info<< "Adding sliding interface zones for curtain of valve "
<< valveI + 1 << endl;
pz[nPointZones] =
new pointZone
(
"cutPointsV" + Foam::name(valveI + 1),
labelList(0),
nPointZones,
pointZones()
);
nPointZones++;
const polyPatch& cylCurtain =
boundaryMesh()
[valves_[valveI].curtainInCylinderPatchID().index()];
labelList cylCurtainLabels(cylCurtain.size(), cylCurtain.start());
forAll (cylCurtainLabels, i)
{
cylCurtainLabels[i] += i;
}
fz[nFaceZones] =
new faceZone
(
"curtainCylZoneV" + Foam::name(valveI + 1),
cylCurtainLabels,
boolList(cylCurtainLabels.size(), false),
nFaceZones,
faceZones()
);
nFaceZones++;
const polyPatch& portCurtain =
boundaryMesh()
[valves_[valveI].curtainInPortPatchID().index()];
labelList portCurtainLabels
(
portCurtain.size(),
portCurtain.start()
);
forAll (portCurtainLabels, i)
{
portCurtainLabels[i] += i;
}
fz[nFaceZones] =
new faceZone
(
"curtainPortZoneV" + Foam::name(valveI + 1),
portCurtainLabels,
boolList(portCurtainLabels.size(), false),
nFaceZones,
faceZones()
);
nFaceZones++;
// Add empty zone for cut faces
fz[nFaceZones] =
new faceZone
(
"cutFaceZoneV" + Foam::name(valveI + 1),
labelList(0),
boolList(0, false),
nFaceZones,
faceZones()
);
nFaceZones++;
// Create a detach zone
if
(
valves_[valveI].detachInCylinderPatchID().active()
&& valves_[valveI].detachInPortPatchID().active()
&& valves_[valveI].detachFaces().size() > 0
)
{
Info<< "Adding detach boundary for valve "
<< valveI + 1 << endl;
const vectorField& areas = Sf().internalField();
const labelList& df = valves_[valveI].detachFaces();
boolList flip(df.size(), false);
const vector& pistonAxis = piston().cs().axis();
forAll (df, dfI)
{
if (isInternalFace(df[dfI]))
{
if ((areas[df[dfI]] & pistonAxis) > 0)
{
flip[dfI] = true;
}
}
else
{
FatalErrorIn
(
"void simpleEngineTopoFvMesh::"
"addZonesAndModifiers()"
) << "found boundary face in valve detach definition"
<< " for valve " << valveI + 1
<< ". This is not allowed. Detach faces: "
<< df << " nInternalFaces: " << nInternalFaces()
<< abort(FatalError);
}
}
// Add detach face zone
fz[nFaceZones] =
new faceZone
(
"detachFaceZoneV" + Foam::name(valveI + 1),
df,
flip,
nFaceZones,
faceZones()
);
nFaceZones++;
}
}
void Foam::movingConeTopoFvMesh::addZonesAndModifiers()
{
// Add zones and modifiers for motion action
if
(
pointZones().size()
|| faceZones().size()
|| cellZones().size()
|| topoChanger_.size()
)
{
Info<< "void movingConeTopoFvMesh::addZonesAndModifiers() : "
<< "Zones and modifiers already present. Skipping."
<< endl;
return;
}
Info<< "Time = " << time().timeName() << endl
<< "Adding zones and modifiers to the mesh" << endl;
const vectorField& fc = faceCentres();
const vectorField& fa = faceAreas();
labelList zone1(fc.size());
boolList flipZone1(fc.size(), false);
label nZoneFaces1 = 0;
labelList zone2(fc.size());
boolList flipZone2(fc.size(), false);
label nZoneFaces2 = 0;
forAll(fc, faceI)
{
if
(
fc[faceI].x() > -0.003501
&& fc[faceI].x() < -0.003499
)
{
if ((fa[faceI] & vector(1, 0, 0)) < 0)
{
flipZone1[nZoneFaces1] = true;
}
zone1[nZoneFaces1] = faceI;
Info<< "face " << faceI << " for zone 1. Flip: "
<< flipZone1[nZoneFaces1] << endl;
nZoneFaces1++;
}
else if
(
fc[faceI].x() > -0.00701
&& fc[faceI].x() < -0.00699
)
{
zone2[nZoneFaces2] = faceI;
if ((fa[faceI] & vector(1, 0, 0)) > 0)
{
flipZone2[nZoneFaces2] = true;
}
Info<< "face " << faceI << " for zone 2. Flip: "
<< flipZone2[nZoneFaces2] << endl;
nZoneFaces2++;
}
}
zone1.setSize(nZoneFaces1);
flipZone1.setSize(nZoneFaces1);
zone2.setSize(nZoneFaces2);
flipZone2.setSize(nZoneFaces2);
Info<< "zone: " << zone1 << endl;
Info<< "zone: " << zone2 << endl;
List<pointZone*> pz(0);
List<faceZone*> fz(2);
List<cellZone*> cz(0);
label nFz = 0;
fz[nFz] =
new faceZone
(
"rightExtrusionFaces",
zone1,
flipZone1,
nFz,
faceZones()
);
nFz++;
fz[nFz] =
new faceZone
(
"leftExtrusionFaces",
zone2,
flipZone2,
nFz,
faceZones()
);
nFz++;
fz.setSize(nFz);
Info<< "Adding mesh zones." << endl;
addZones(pz, fz, cz);
// Add layer addition/removal interfaces
List<polyMeshModifier*> tm(2);
label nMods = 0;
tm[nMods] =
new layerAdditionRemoval
(
"right",
nMods,
topoChanger_,
"rightExtrusionFaces",
readScalar
(
motionDict_.subDict("right").lookup("minThickness")
),
readScalar
(
motionDict_.subDict("right").lookup("maxThickness")
)
);
nMods++;
tm[nMods] = new layerAdditionRemoval
(
"left",
nMods,
topoChanger_,
"leftExtrusionFaces",
readScalar
(
motionDict_.subDict("left").lookup("minThickness")
),
readScalar
(
motionDict_.subDict("left").lookup("maxThickness")
)
);
nMods++;
tm.setSize(nMods);
Info<< "Adding " << nMods << " mesh modifiers" << endl;
topoChanger_.addTopologyModifiers(tm);
write();
}